Starting phenix.real_space_refine on Sat Aug 8 05:32:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yml_73110/08_2026/9yml_73110.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yml_73110/08_2026/9yml_73110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yml_73110/08_2026/9yml_73110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yml_73110/08_2026/9yml_73110.map" model { file = "/net/cci-nas-00/data/ceres_data/9yml_73110/08_2026/9yml_73110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yml_73110/08_2026/9yml_73110.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 15912 2.51 5 N 4290 2.21 5 O 5175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25515 Number of models: 1 Model: "" Number of chains: 34 Chain: "G" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 984 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3501 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, E, D, F, J, O, K, P, M, Q, N, R, d, n, h, r Time building chain proxies: 5.51, per 1000 atoms: 0.22 Number of scatterers: 25515 At special positions: 0 Unit cell: (158.688, 151.38, 174.348, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 5175 8.00 N 4290 7.00 C 15912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA T 3 " - " MAN T 7 " " MAN T 4 " - " MAN T 5 " " BMA d 3 " - " MAN d 7 " " MAN d 4 " - " MAN d 5 " " BMA n 3 " - " MAN n 7 " " MAN n 4 " - " MAN n 5 " ALPHA1-6 " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 6 " " BMA X 3 " - " MAN X 4 " " BMA d 3 " - " MAN d 4 " " MAN d 4 " - " MAN d 6 " " BMA h 3 " - " MAN h 4 " " BMA n 3 " - " MAN n 4 " " MAN n 4 " - " MAN n 6 " " BMA r 3 " - " MAN r 4 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 392 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 160 " " NAG A 608 " - " ASN A 301 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 137 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 355 " " NAG C 607 " - " ASN C 160 " " NAG C 608 " - " ASN C 301 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 339 " " NAG E 603 " - " ASN E 392 " " NAG E 604 " - " ASN E 137 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 355 " " NAG E 607 " - " ASN E 160 " " NAG E 608 " - " ASN E 301 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG S 1 " - " ASN A 448 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 156 " " NAG V 1 " - " ASN A 197 " " NAG W 1 " - " ASN A 234 " " NAG X 1 " - " ASN A 262 " " NAG Y 1 " - " ASN A 386 " " NAG Z 1 " - " ASN A 88 " " NAG a 1 " - " ASN A 276 " " NAG b 1 " - " ASN B 611 " " NAG c 1 " - " ASN C 448 " " NAG d 1 " - " ASN C 332 " " NAG e 1 " - " ASN C 156 " " NAG f 1 " - " ASN C 197 " " NAG g 1 " - " ASN C 234 " " NAG h 1 " - " ASN C 262 " " NAG i 1 " - " ASN C 386 " " NAG j 1 " - " ASN C 88 " " NAG k 1 " - " ASN C 276 " " NAG l 1 " - " ASN D 611 " " NAG m 1 " - " ASN E 448 " " NAG n 1 " - " ASN E 332 " " NAG o 1 " - " ASN E 156 " " NAG p 1 " - " ASN E 197 " " NAG q 1 " - " ASN E 234 " " NAG r 1 " - " ASN E 262 " " NAG s 1 " - " ASN E 386 " " NAG t 1 " - " ASN E 88 " " NAG u 1 " - " ASN E 276 " " NAG v 1 " - " ASN F 611 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 959.3 milliseconds 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5664 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 57 sheets defined 15.3% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.590A pdb=" N PHE G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.546A pdb=" N LYS G 64 " --> pdb=" O ASP G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'H' and resid 63 through 67 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.931A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.960A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.154A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.673A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.873A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.591A pdb=" N PHE J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.546A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'K' and resid 63 through 67 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.931A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.960A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.153A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.673A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.873A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.591A pdb=" N PHE O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.546A pdb=" N LYS O 64 " --> pdb=" O ASP O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'P' and resid 63 through 67 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.931A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.960A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.153A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.673A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.873A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.623A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE G 102 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.623A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AA5, first strand: chain 'H' and resid 50 through 51 removed outlier: 3.596A pdb=" N ILE H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP H 35 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN H 39 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 97 through 99 Processing sheet with id=AA7, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AA8, first strand: chain 'I' and resid 45 through 48 removed outlier: 5.698A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 23 through 24 removed outlier: 3.634A pdb=" N CYS L 23 " --> pdb=" O ALA L 71 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 44 through 48 removed outlier: 5.558A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.555A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.085A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.580A pdb=" N ALA A 433 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.145A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.872A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.311A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.872A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 302 through 312 removed outlier: 7.112A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 321 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.622A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N MET J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE J 102 " --> pdb=" O THR J 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.622A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N MET J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 21 through 23 Processing sheet with id=AC6, first strand: chain 'K' and resid 50 through 51 removed outlier: 3.597A pdb=" N ILE K 51 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP K 35 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN K 39 " --> pdb=" O THR K 89 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 97 through 99 Processing sheet with id=AC8, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'M' and resid 45 through 48 removed outlier: 5.697A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 23 through 24 removed outlier: 3.634A pdb=" N CYS N 23 " --> pdb=" O ALA N 71 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 44 through 48 removed outlier: 5.558A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP N 85 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.555A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.086A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AD6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD8, first strand: chain 'C' and resid 200 through 203 removed outlier: 3.580A pdb=" N ALA C 433 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.145A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.872A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.765A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.021A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 271 through 274 removed outlier: 11.311A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.021A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.765A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.872A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 302 through 312 removed outlier: 7.113A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 321 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.623A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N MET O 34 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE O 102 " --> pdb=" O THR O 94 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.623A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N MET O 34 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 21 through 23 Processing sheet with id=AE7, first strand: chain 'P' and resid 50 through 51 removed outlier: 3.596A pdb=" N ILE P 51 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP P 35 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN P 39 " --> pdb=" O THR P 89 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 97 through 99 Processing sheet with id=AE9, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AF1, first strand: chain 'Q' and resid 45 through 48 removed outlier: 5.697A pdb=" N LEU Q 46 " --> pdb=" O GLN Q 37 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN Q 37 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 23 through 24 removed outlier: 3.634A pdb=" N CYS R 23 " --> pdb=" O ALA R 71 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR R 70 " --> pdb=" O SER R 67 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 44 through 48 removed outlier: 5.558A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP R 85 " --> pdb=" O GLN R 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.555A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.085A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AF7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AF8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AF9, first strand: chain 'E' and resid 200 through 203 removed outlier: 3.580A pdb=" N ALA E 433 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.145A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.872A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.765A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.021A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 271 through 274 removed outlier: 11.311A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.021A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.765A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.872A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 302 through 312 removed outlier: 7.113A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 834 hydrogen bonds defined for protein. 2259 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.68 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7871 1.34 - 1.46: 4959 1.46 - 1.58: 13006 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 26022 Sorted by residual: bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N GLN K 1 " pdb=" CA GLN K 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N GLN P 1 " pdb=" CA GLN P 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N SER R 1 " pdb=" CA SER R 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N SER N 1 " pdb=" CA SER N 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 ... (remaining 26017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 34161 1.56 - 3.13: 861 3.13 - 4.69: 240 4.69 - 6.26: 54 6.26 - 7.82: 15 Bond angle restraints: 35331 Sorted by residual: angle pdb=" CA ASN A 156 " pdb=" C ASN A 156 " pdb=" N CYS A 157 " ideal model delta sigma weight residual 115.85 119.74 -3.89 1.29e+00 6.01e-01 9.08e+00 angle pdb=" CA ASN E 156 " pdb=" C ASN E 156 " pdb=" N CYS E 157 " ideal model delta sigma weight residual 115.85 119.72 -3.87 1.29e+00 6.01e-01 9.01e+00 angle pdb=" CA ASN C 156 " pdb=" C ASN C 156 " pdb=" N CYS C 157 " ideal model delta sigma weight residual 115.85 119.71 -3.86 1.29e+00 6.01e-01 8.96e+00 angle pdb=" N SER C 463 " pdb=" CA SER C 463 " pdb=" CB SER C 463 " ideal model delta sigma weight residual 114.17 110.79 3.38 1.14e+00 7.69e-01 8.77e+00 angle pdb=" N SER E 463 " pdb=" CA SER E 463 " pdb=" CB SER E 463 " ideal model delta sigma weight residual 114.17 110.82 3.35 1.14e+00 7.69e-01 8.63e+00 ... (remaining 35326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 15696 17.81 - 35.63: 863 35.63 - 53.44: 268 53.44 - 71.25: 39 71.25 - 89.06: 42 Dihedral angle restraints: 16908 sinusoidal: 8058 harmonic: 8850 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -122.38 36.38 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -122.37 36.37 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -122.37 36.37 1 1.00e+01 1.00e-02 1.87e+01 ... (remaining 16905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 4260 0.177 - 0.355: 12 0.355 - 0.532: 0 0.532 - 0.710: 0 0.710 - 0.887: 3 Chirality restraints: 4275 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN A 448 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 448 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" C1 NAG m 1 " pdb=" ND2 ASN E 448 " pdb=" C2 NAG m 1 " pdb=" O5 NAG m 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.96e+01 ... (remaining 4272 not shown) Planarity restraints: 4428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 98 " -0.024 2.00e-02 2.50e+03 1.65e-02 4.77e+00 pdb=" CG PHE L 98 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE L 98 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE L 98 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE L 98 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 98 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE L 98 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 98 " 0.024 2.00e-02 2.50e+03 1.65e-02 4.77e+00 pdb=" CG PHE N 98 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE N 98 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE N 98 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE N 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 98 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE N 98 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 98 " 0.024 2.00e-02 2.50e+03 1.65e-02 4.76e+00 pdb=" CG PHE R 98 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE R 98 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 98 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 98 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 98 " 0.015 2.00e-02 2.50e+03 ... (remaining 4425 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 6 2.12 - 2.81: 6799 2.81 - 3.51: 33884 3.51 - 4.20: 60980 4.20 - 4.90: 106265 Nonbonded interactions: 207934 Sorted by model distance: nonbonded pdb=" NH2 ARG J 53 " pdb=" OD2 ASP F 659 " model vdw 1.421 3.120 nonbonded pdb=" OD2 ASP B 659 " pdb=" NH2 ARG O 53 " model vdw 1.421 3.120 nonbonded pdb=" NH2 ARG G 53 " pdb=" OD2 ASP D 659 " model vdw 1.421 3.120 nonbonded pdb=" OH TYR J 100F" pdb=" OD1 ASP F 664 " model vdw 1.996 3.040 nonbonded pdb=" OH TYR G 100F" pdb=" OD1 ASP D 664 " model vdw 1.996 3.040 ... (remaining 207929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'T' selection = chain 'd' selection = chain 'n' } ncs_group { reference = chain 'X' selection = chain 'h' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.000 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26178 Z= 0.185 Angle : 0.755 13.461 35754 Z= 0.350 Chirality : 0.052 0.887 4275 Planarity : 0.004 0.040 4368 Dihedral : 12.911 89.063 11109 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.93 % Favored : 94.97 % Rotamer: Outliers : 0.90 % Allowed : 5.56 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 3042 helix: 1.78 (0.27), residues: 387 sheet: -0.49 (0.18), residues: 744 loop : -1.46 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 504 TYR 0.018 0.001 TYR Q 49 PHE 0.033 0.002 PHE N 98 TRP 0.009 0.001 TRP A 96 HIS 0.005 0.001 HIS N 95B Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (26022) covalent geometry : angle 0.68889 / 0.34 (35331) SS BOND : bond 0.00351 / 0.20 ( 45) SS BOND : angle 0.89503 / 0.64 ( 90) hydrogen bonds : bond 0.12155 / 8.55 ( 777) hydrogen bonds : angle 6.57022 / 4.51 ( 2259) link_ALPHA1-3 : bond 0.00736 / 0.41 ( 6) link_ALPHA1-3 : angle 3.15539 / 1.80 ( 18) link_ALPHA1-6 : bond 0.00392 / 0.27 ( 9) link_ALPHA1-6 : angle 1.90584 / 1.14 ( 27) link_BETA1-4 : bond 0.00644 / 0.52 ( 36) link_BETA1-4 : angle 2.74991 / 1.93 ( 108) link_NAG-ASN : bond 0.00546 / 0.37 ( 60) link_NAG-ASN : angle 3.67850 / 2.53 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 403 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 ASP cc_start: 0.8404 (t0) cc_final: 0.7854 (t0) REVERT: I 31 ASN cc_start: 0.8730 (p0) cc_final: 0.8488 (p0) REVERT: I 60 ASP cc_start: 0.8265 (p0) cc_final: 0.8011 (p0) REVERT: I 79 GLN cc_start: 0.8016 (mp10) cc_final: 0.7453 (mp10) REVERT: L 97 PHE cc_start: 0.5882 (t80) cc_final: 0.5054 (t80) REVERT: A 92 GLU cc_start: 0.8524 (tt0) cc_final: 0.8304 (tp30) REVERT: A 135 THR cc_start: 0.4904 (OUTLIER) cc_final: 0.4610 (p) REVERT: A 192 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8390 (ptt-90) REVERT: A 368 ASP cc_start: 0.7177 (t0) cc_final: 0.6959 (t0) REVERT: B 632 ASP cc_start: 0.8626 (t0) cc_final: 0.8320 (t0) REVERT: J 72 ASP cc_start: 0.8467 (t0) cc_final: 0.7949 (t0) REVERT: K 77 GLN cc_start: 0.7287 (mt0) cc_final: 0.6989 (mp10) REVERT: M 31 ASN cc_start: 0.8720 (p0) cc_final: 0.8458 (p0) REVERT: M 53 GLN cc_start: 0.8904 (mp10) cc_final: 0.8179 (mp10) REVERT: M 79 GLN cc_start: 0.7948 (mp10) cc_final: 0.7448 (mp-120) REVERT: N 89 GLN cc_start: 0.5907 (tp40) cc_final: 0.5485 (tp40) REVERT: N 97 PHE cc_start: 0.5788 (t80) cc_final: 0.5556 (t80) REVERT: C 92 GLU cc_start: 0.8491 (tt0) cc_final: 0.8283 (tp30) REVERT: D 624 ASP cc_start: 0.9055 (m-30) cc_final: 0.8834 (m-30) REVERT: O 6 GLU cc_start: 0.8491 (mp0) cc_final: 0.8186 (mp0) REVERT: O 72 ASP cc_start: 0.8272 (t0) cc_final: 0.7798 (t0) REVERT: Q 31 ASN cc_start: 0.8697 (p0) cc_final: 0.8439 (p0) REVERT: Q 45 LYS cc_start: 0.9045 (tttp) cc_final: 0.8813 (tttm) REVERT: Q 53 GLN cc_start: 0.8827 (mp10) cc_final: 0.8509 (mp10) REVERT: Q 79 GLN cc_start: 0.8060 (mp10) cc_final: 0.7533 (mp10) REVERT: R 46 LEU cc_start: 0.6868 (pt) cc_final: 0.6537 (mp) REVERT: R 97 PHE cc_start: 0.5764 (t80) cc_final: 0.5374 (t80) REVERT: E 92 GLU cc_start: 0.8501 (tt0) cc_final: 0.8292 (tp30) REVERT: E 246 GLN cc_start: 0.7686 (tp-100) cc_final: 0.7413 (mm110) REVERT: E 368 ASP cc_start: 0.7243 (t0) cc_final: 0.7041 (t0) outliers start: 24 outliers final: 12 residues processed: 427 average time/residue: 0.1652 time to fit residues: 113.1025 Evaluate side-chains 342 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 328 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain E residue 247 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 69 ASN L 32 ASN L 51 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 543 ASN J 3 GLN N 32 ASN N 51 ASN C 94 ASN C 374 HIS D 625 ASN O 105 GLN P 77 GLN R 32 ASN R 51 ASN E 374 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.161370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115643 restraints weight = 38342.769| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.33 r_work: 0.3234 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 26178 Z= 0.218 Angle : 0.724 10.629 35754 Z= 0.338 Chirality : 0.048 0.239 4275 Planarity : 0.005 0.037 4368 Dihedral : 10.258 83.201 5634 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.00 % Rotamer: Outliers : 1.88 % Allowed : 10.29 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.15), residues: 3042 helix: 1.29 (0.26), residues: 417 sheet: -0.60 (0.17), residues: 810 loop : -1.43 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 542 TYR 0.021 0.002 TYR M 49 PHE 0.023 0.002 PHE R 98 TRP 0.012 0.001 TRP A 96 HIS 0.005 0.001 HIS H 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (26022) covalent geometry : angle 0.66721 / 0.32 (35331) SS BOND : bond 0.00444 / 0.29 ( 45) SS BOND : angle 1.16215 / 0.72 ( 90) hydrogen bonds : bond 0.04404 / 2.96 ( 777) hydrogen bonds : angle 5.68522 / 3.88 ( 2259) link_ALPHA1-3 : bond 0.00853 / 0.46 ( 6) link_ALPHA1-3 : angle 3.26938 / 1.82 ( 18) link_ALPHA1-6 : bond 0.00466 / 0.33 ( 9) link_ALPHA1-6 : angle 1.95475 / 1.25 ( 27) link_BETA1-4 : bond 0.00696 / 0.52 ( 36) link_BETA1-4 : angle 2.67433 / 1.84 ( 108) link_NAG-ASN : bond 0.00637 / 0.38 ( 60) link_NAG-ASN : angle 3.20281 / 2.15 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 336 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 ASP cc_start: 0.8592 (t0) cc_final: 0.8217 (t0) REVERT: I 79 GLN cc_start: 0.8199 (mp10) cc_final: 0.7543 (mp10) REVERT: L 97 PHE cc_start: 0.6040 (t80) cc_final: 0.5223 (t80) REVERT: A 135 THR cc_start: 0.4964 (OUTLIER) cc_final: 0.4658 (p) REVERT: A 448 ASN cc_start: 0.8400 (p0) cc_final: 0.8027 (p0) REVERT: J 43 LYS cc_start: 0.8201 (mptt) cc_final: 0.7969 (mtmt) REVERT: J 72 ASP cc_start: 0.8629 (t0) cc_final: 0.8288 (t0) REVERT: K 56 VAL cc_start: 0.3872 (OUTLIER) cc_final: 0.3614 (m) REVERT: K 77 GLN cc_start: 0.7414 (mt0) cc_final: 0.7110 (mp10) REVERT: M 31 ASN cc_start: 0.8604 (p0) cc_final: 0.8401 (p0) REVERT: M 53 GLN cc_start: 0.8986 (mp10) cc_final: 0.8393 (mp10) REVERT: M 79 GLN cc_start: 0.8123 (mp10) cc_final: 0.7618 (mp10) REVERT: N 89 GLN cc_start: 0.5551 (tp40) cc_final: 0.5243 (tp40) REVERT: N 97 PHE cc_start: 0.5955 (t80) cc_final: 0.5673 (t80) REVERT: C 129 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8523 (mt) REVERT: C 308 ARG cc_start: 0.8479 (mtt90) cc_final: 0.8101 (mtp85) REVERT: D 624 ASP cc_start: 0.9033 (m-30) cc_final: 0.8771 (m-30) REVERT: O 72 ASP cc_start: 0.8563 (t0) cc_final: 0.8175 (t0) REVERT: P 77 GLN cc_start: 0.7274 (mt0) cc_final: 0.7019 (mp10) REVERT: Q 31 ASN cc_start: 0.8651 (p0) cc_final: 0.8449 (p0) REVERT: Q 79 GLN cc_start: 0.8264 (mp10) cc_final: 0.7716 (mp10) REVERT: R 97 PHE cc_start: 0.5913 (t80) cc_final: 0.5702 (t80) outliers start: 50 outliers final: 28 residues processed: 370 average time/residue: 0.1584 time to fit residues: 95.1269 Evaluate side-chains 332 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 301 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 172 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 30 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 135 optimal weight: 40.0000 chunk 275 optimal weight: 6.9990 chunk 213 optimal weight: 20.0000 chunk 110 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS I 69 ASN A 67 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS K 52 HIS C 67 ASN P 52 HIS E 67 ASN F 543 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.157629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.111036 restraints weight = 38694.393| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.45 r_work: 0.3190 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 26178 Z= 0.260 Angle : 0.725 9.266 35754 Z= 0.341 Chirality : 0.048 0.236 4275 Planarity : 0.004 0.034 4368 Dihedral : 10.298 80.726 5622 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.65 % Favored : 94.25 % Rotamer: Outliers : 2.70 % Allowed : 11.56 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.15), residues: 3042 helix: 1.12 (0.26), residues: 417 sheet: -0.60 (0.17), residues: 783 loop : -1.44 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 542 TYR 0.025 0.002 TYR M 49 PHE 0.022 0.002 PHE L 98 TRP 0.013 0.002 TRP A 96 HIS 0.011 0.001 HIS P 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.26 (26022) covalent geometry : angle 0.66873 / 0.33 (35331) SS BOND : bond 0.00477 / 0.30 ( 45) SS BOND : angle 1.43853 / 0.85 ( 90) hydrogen bonds : bond 0.04570 / 3.09 ( 777) hydrogen bonds : angle 5.63761 / 3.85 ( 2259) link_ALPHA1-3 : bond 0.00882 / 0.46 ( 6) link_ALPHA1-3 : angle 3.40520 / 1.90 ( 18) link_ALPHA1-6 : bond 0.00464 / 0.32 ( 9) link_ALPHA1-6 : angle 2.02194 / 1.27 ( 27) link_BETA1-4 : bond 0.00652 / 0.47 ( 36) link_BETA1-4 : angle 2.57032 / 1.79 ( 108) link_NAG-ASN : bond 0.00649 / 0.41 ( 60) link_NAG-ASN : angle 3.12368 / 2.09 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 320 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 LEU cc_start: 0.8675 (mp) cc_final: 0.8405 (mt) REVERT: G 72 ASP cc_start: 0.8528 (t0) cc_final: 0.8248 (t0) REVERT: L 97 PHE cc_start: 0.6091 (t80) cc_final: 0.5437 (t80) REVERT: A 129 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8519 (mt) REVERT: B 632 ASP cc_start: 0.8718 (t0) cc_final: 0.8430 (t0) REVERT: J 61 ASP cc_start: 0.8619 (t0) cc_final: 0.8284 (m-30) REVERT: J 72 ASP cc_start: 0.8589 (t0) cc_final: 0.8372 (t0) REVERT: J 108 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8537 (tt) REVERT: K 77 GLN cc_start: 0.7270 (mt0) cc_final: 0.7036 (mp10) REVERT: M 31 ASN cc_start: 0.8688 (p0) cc_final: 0.8416 (p0) REVERT: M 53 GLN cc_start: 0.9036 (mp10) cc_final: 0.8369 (mp10) REVERT: M 79 GLN cc_start: 0.8262 (mp10) cc_final: 0.7787 (mp10) REVERT: N 89 GLN cc_start: 0.5474 (tp40) cc_final: 0.5204 (tp40) REVERT: N 97 PHE cc_start: 0.5957 (t80) cc_final: 0.5736 (t80) REVERT: C 129 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8368 (mt) REVERT: D 624 ASP cc_start: 0.9057 (m-30) cc_final: 0.8754 (m-30) REVERT: O 72 ASP cc_start: 0.8594 (t0) cc_final: 0.8175 (t0) REVERT: P 77 GLN cc_start: 0.7199 (mt0) cc_final: 0.6909 (mp10) REVERT: Q 31 ASN cc_start: 0.8725 (p0) cc_final: 0.8479 (p0) REVERT: Q 79 GLN cc_start: 0.8343 (mp10) cc_final: 0.7754 (mp10) outliers start: 72 outliers final: 41 residues processed: 372 average time/residue: 0.1528 time to fit residues: 93.4270 Evaluate side-chains 339 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 320 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 49 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 286 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN J 3 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS P 33 HIS E 85 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.158818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111864 restraints weight = 38492.331| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.47 r_work: 0.3208 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26178 Z= 0.188 Angle : 0.673 8.941 35754 Z= 0.317 Chirality : 0.046 0.221 4275 Planarity : 0.004 0.036 4368 Dihedral : 10.112 78.210 5621 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 2.14 % Allowed : 13.21 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.15), residues: 3042 helix: 1.29 (0.27), residues: 417 sheet: -0.68 (0.17), residues: 834 loop : -1.40 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 542 TYR 0.018 0.001 TYR M 49 PHE 0.032 0.002 PHE R 97 TRP 0.012 0.001 TRP A 96 HIS 0.007 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (26022) covalent geometry : angle 0.62145 / 0.31 (35331) SS BOND : bond 0.00530 / 0.36 ( 45) SS BOND : angle 1.40137 / 0.83 ( 90) hydrogen bonds : bond 0.04111 / 2.77 ( 777) hydrogen bonds : angle 5.44888 / 3.72 ( 2259) link_ALPHA1-3 : bond 0.00846 / 0.43 ( 6) link_ALPHA1-3 : angle 3.19599 / 1.78 ( 18) link_ALPHA1-6 : bond 0.00504 / 0.35 ( 9) link_ALPHA1-6 : angle 2.10146 / 1.33 ( 27) link_BETA1-4 : bond 0.00669 / 0.50 ( 36) link_BETA1-4 : angle 2.45575 / 1.72 ( 108) link_NAG-ASN : bond 0.00536 / 0.32 ( 60) link_NAG-ASN : angle 2.82070 / 1.88 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 316 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 ASP cc_start: 0.8487 (t0) cc_final: 0.8245 (t0) REVERT: H 77 GLN cc_start: 0.7863 (mt0) cc_final: 0.7606 (mp10) REVERT: I 79 GLN cc_start: 0.8282 (mp10) cc_final: 0.7516 (mp10) REVERT: A 129 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8517 (mt) REVERT: J 72 ASP cc_start: 0.8533 (t0) cc_final: 0.8331 (t0) REVERT: J 108 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8517 (tt) REVERT: M 31 ASN cc_start: 0.8666 (p0) cc_final: 0.8384 (p0) REVERT: M 53 GLN cc_start: 0.8995 (mp10) cc_final: 0.8381 (mp10) REVERT: M 79 GLN cc_start: 0.8246 (mp10) cc_final: 0.7838 (mp10) REVERT: N 89 GLN cc_start: 0.5431 (tp40) cc_final: 0.5172 (tp40) REVERT: N 97 PHE cc_start: 0.5983 (t80) cc_final: 0.5766 (t80) REVERT: C 129 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8450 (mt) REVERT: C 161 MET cc_start: 0.9155 (tpt) cc_final: 0.8799 (tpt) REVERT: D 624 ASP cc_start: 0.9009 (m-30) cc_final: 0.8758 (m-30) REVERT: O 72 ASP cc_start: 0.8605 (t0) cc_final: 0.8218 (t0) REVERT: Q 31 ASN cc_start: 0.8707 (p0) cc_final: 0.8469 (p0) REVERT: Q 79 GLN cc_start: 0.8358 (mp10) cc_final: 0.7957 (mp10) outliers start: 57 outliers final: 38 residues processed: 359 average time/residue: 0.1597 time to fit residues: 93.3643 Evaluate side-chains 339 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 298 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 94 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 162 optimal weight: 0.0270 chunk 238 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 188 optimal weight: 0.0770 chunk 145 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN G 105 GLN H 33 HIS I 69 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.161229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114626 restraints weight = 38104.648| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.42 r_work: 0.3255 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26178 Z= 0.118 Angle : 0.615 8.528 35754 Z= 0.290 Chirality : 0.045 0.241 4275 Planarity : 0.004 0.041 4368 Dihedral : 9.762 75.358 5621 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.14 % Allowed : 13.55 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.15), residues: 3042 helix: 1.70 (0.27), residues: 417 sheet: -0.53 (0.17), residues: 831 loop : -1.45 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 542 TYR 0.010 0.001 TYR M 49 PHE 0.025 0.001 PHE N 98 TRP 0.012 0.001 TRP A 96 HIS 0.018 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (26022) covalent geometry : angle 0.56992 / 0.28 (35331) SS BOND : bond 0.00372 / 0.22 ( 45) SS BOND : angle 1.26809 / 0.75 ( 90) hydrogen bonds : bond 0.03595 / 2.41 ( 777) hydrogen bonds : angle 5.22944 / 3.57 ( 2259) link_ALPHA1-3 : bond 0.00904 / 0.47 ( 6) link_ALPHA1-3 : angle 2.97003 / 1.66 ( 18) link_ALPHA1-6 : bond 0.00493 / 0.34 ( 9) link_ALPHA1-6 : angle 2.18410 / 1.34 ( 27) link_BETA1-4 : bond 0.00695 / 0.52 ( 36) link_BETA1-4 : angle 2.29252 / 1.62 ( 108) link_NAG-ASN : bond 0.00447 / 0.26 ( 60) link_NAG-ASN : angle 2.40868 / 1.60 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 327 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 ASP cc_start: 0.8428 (t0) cc_final: 0.8170 (t0) REVERT: G 87 THR cc_start: 0.8752 (p) cc_final: 0.8545 (p) REVERT: H 52 HIS cc_start: 0.6459 (t70) cc_final: 0.6197 (t70) REVERT: H 77 GLN cc_start: 0.7999 (mt0) cc_final: 0.7790 (mp10) REVERT: I 79 GLN cc_start: 0.8165 (mp10) cc_final: 0.7394 (mp10) REVERT: A 129 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8447 (mt) REVERT: A 192 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8320 (ptt-90) REVERT: J 72 ASP cc_start: 0.8485 (t0) cc_final: 0.8242 (t0) REVERT: J 108 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8515 (tt) REVERT: K 77 GLN cc_start: 0.7816 (mt0) cc_final: 0.7493 (mp10) REVERT: M 31 ASN cc_start: 0.8635 (p0) cc_final: 0.8386 (p0) REVERT: M 53 GLN cc_start: 0.8952 (mp10) cc_final: 0.8359 (mp10) REVERT: M 79 GLN cc_start: 0.8183 (mp10) cc_final: 0.7618 (mp10) REVERT: N 89 GLN cc_start: 0.5780 (tp40) cc_final: 0.5579 (tp40) REVERT: N 97 PHE cc_start: 0.6025 (t80) cc_final: 0.5812 (t80) REVERT: C 129 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8395 (mt) REVERT: C 161 MET cc_start: 0.9120 (tpt) cc_final: 0.8812 (tpt) REVERT: D 624 ASP cc_start: 0.8996 (m-30) cc_final: 0.8685 (m-30) REVERT: O 72 ASP cc_start: 0.8582 (t0) cc_final: 0.8202 (t0) REVERT: P 77 GLN cc_start: 0.7225 (mp10) cc_final: 0.6835 (tt0) REVERT: Q 31 ASN cc_start: 0.8698 (p0) cc_final: 0.8476 (p0) REVERT: Q 79 GLN cc_start: 0.8298 (mp10) cc_final: 0.7889 (mp10) outliers start: 57 outliers final: 32 residues processed: 371 average time/residue: 0.1457 time to fit residues: 87.8248 Evaluate side-chains 338 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 33 HIS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 320 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 41 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 292 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 256 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 HIS B 652 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS D 591 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN F 543 ASN F 591 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.155802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.109071 restraints weight = 38811.783| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.15 r_work: 0.3165 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 26178 Z= 0.368 Angle : 0.793 10.752 35754 Z= 0.377 Chirality : 0.051 0.255 4275 Planarity : 0.005 0.041 4368 Dihedral : 9.982 76.447 5621 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.64 % Favored : 93.29 % Rotamer: Outliers : 2.55 % Allowed : 14.41 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.14), residues: 3042 helix: 0.49 (0.26), residues: 450 sheet: -0.87 (0.17), residues: 822 loop : -1.65 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 542 TYR 0.035 0.002 TYR M 49 PHE 0.022 0.003 PHE N 98 TRP 0.014 0.002 TRP J 103 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00874 / 0.37 (26022) covalent geometry : angle 0.73669 / 0.36 (35331) SS BOND : bond 0.00788 / 0.52 ( 45) SS BOND : angle 2.12274 / 1.35 ( 90) hydrogen bonds : bond 0.04897 / 3.30 ( 777) hydrogen bonds : angle 5.61284 / 3.84 ( 2259) link_ALPHA1-3 : bond 0.00734 / 0.39 ( 6) link_ALPHA1-3 : angle 3.58132 / 2.00 ( 18) link_ALPHA1-6 : bond 0.00494 / 0.33 ( 9) link_ALPHA1-6 : angle 1.94053 / 1.19 ( 27) link_BETA1-4 : bond 0.00701 / 0.54 ( 36) link_BETA1-4 : angle 2.58235 / 1.82 ( 108) link_NAG-ASN : bond 0.00756 / 0.51 ( 60) link_NAG-ASN : angle 3.18437 / 2.13 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 297 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 ASP cc_start: 0.8530 (t0) cc_final: 0.8257 (t0) REVERT: H 77 GLN cc_start: 0.7995 (mt0) cc_final: 0.7731 (mp10) REVERT: L 97 PHE cc_start: 0.6457 (t80) cc_final: 0.6196 (t80) REVERT: A 129 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8568 (mt) REVERT: A 166 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8337 (ttp80) REVERT: B 632 ASP cc_start: 0.8727 (t0) cc_final: 0.8420 (t0) REVERT: J 72 ASP cc_start: 0.8643 (t0) cc_final: 0.8423 (t0) REVERT: J 108 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8496 (tt) REVERT: K 77 GLN cc_start: 0.7737 (mt0) cc_final: 0.7363 (mp10) REVERT: M 31 ASN cc_start: 0.8719 (p0) cc_final: 0.8412 (p0) REVERT: M 53 GLN cc_start: 0.9071 (mp10) cc_final: 0.8657 (mp10) REVERT: M 79 GLN cc_start: 0.8209 (mp10) cc_final: 0.7696 (mp-120) REVERT: N 27 THR cc_start: 0.4215 (m) cc_final: 0.4003 (t) REVERT: N 89 GLN cc_start: 0.5609 (tp40) cc_final: 0.5364 (tp40) REVERT: N 97 PHE cc_start: 0.6108 (t80) cc_final: 0.5856 (t80) REVERT: C 129 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8425 (mt) REVERT: O 72 ASP cc_start: 0.8614 (t0) cc_final: 0.8219 (t0) REVERT: P 77 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6969 (mp10) REVERT: Q 31 ASN cc_start: 0.8788 (p0) cc_final: 0.8519 (p0) REVERT: Q 79 GLN cc_start: 0.8394 (mp10) cc_final: 0.8048 (mp10) REVERT: F 588 ARG cc_start: 0.8630 (mtt90) cc_final: 0.8381 (mtt180) outliers start: 68 outliers final: 53 residues processed: 348 average time/residue: 0.1691 time to fit residues: 94.5330 Evaluate side-chains 350 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 292 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 254 optimal weight: 2.9990 chunk 295 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.159075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112547 restraints weight = 38501.355| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.38 r_work: 0.3225 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26178 Z= 0.154 Angle : 0.649 10.409 35754 Z= 0.307 Chirality : 0.045 0.207 4275 Planarity : 0.004 0.050 4368 Dihedral : 9.648 74.830 5620 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.88 % Allowed : 15.58 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.15), residues: 3042 helix: 1.13 (0.27), residues: 435 sheet: -0.73 (0.17), residues: 843 loop : -1.51 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 542 TYR 0.014 0.001 TYR M 49 PHE 0.024 0.002 PHE N 98 TRP 0.014 0.001 TRP P 35 HIS 0.006 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (26022) covalent geometry : angle 0.59967 / 0.30 (35331) SS BOND : bond 0.00607 / 0.41 ( 45) SS BOND : angle 1.77881 / 1.08 ( 90) hydrogen bonds : bond 0.03922 / 2.64 ( 777) hydrogen bonds : angle 5.32040 / 3.63 ( 2259) link_ALPHA1-3 : bond 0.00864 / 0.44 ( 6) link_ALPHA1-3 : angle 3.04456 / 1.70 ( 18) link_ALPHA1-6 : bond 0.00497 / 0.33 ( 9) link_ALPHA1-6 : angle 2.10458 / 1.29 ( 27) link_BETA1-4 : bond 0.00687 / 0.52 ( 36) link_BETA1-4 : angle 2.37951 / 1.70 ( 108) link_NAG-ASN : bond 0.00438 / 0.27 ( 60) link_NAG-ASN : angle 2.57358 / 1.72 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 316 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 ASP cc_start: 0.8450 (t0) cc_final: 0.8183 (t0) REVERT: H 77 GLN cc_start: 0.8001 (mt0) cc_final: 0.7756 (mp10) REVERT: A 129 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8479 (mt) REVERT: A 166 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8327 (ttp80) REVERT: A 192 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8368 (ptt-90) REVERT: J 72 ASP cc_start: 0.8535 (t0) cc_final: 0.8270 (t0) REVERT: J 108 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8510 (tt) REVERT: K 77 GLN cc_start: 0.7938 (mt0) cc_final: 0.7621 (mp10) REVERT: M 31 ASN cc_start: 0.8639 (p0) cc_final: 0.8380 (p0) REVERT: M 53 GLN cc_start: 0.8979 (mp10) cc_final: 0.8313 (mp10) REVERT: M 79 GLN cc_start: 0.8214 (mp10) cc_final: 0.7687 (mp10) REVERT: N 27 THR cc_start: 0.4676 (m) cc_final: 0.4416 (t) REVERT: N 89 GLN cc_start: 0.5544 (tp40) cc_final: 0.5297 (tp40) REVERT: N 97 PHE cc_start: 0.6138 (t80) cc_final: 0.5901 (t80) REVERT: C 129 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8488 (mt) REVERT: C 161 MET cc_start: 0.9185 (tpt) cc_final: 0.8829 (tpt) REVERT: D 624 ASP cc_start: 0.8827 (m-30) cc_final: 0.8625 (m-30) REVERT: O 72 ASP cc_start: 0.8536 (t0) cc_final: 0.8121 (t0) REVERT: P 77 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: Q 31 ASN cc_start: 0.8725 (p0) cc_final: 0.8479 (p0) REVERT: Q 79 GLN cc_start: 0.8386 (mp10) cc_final: 0.8048 (mp10) outliers start: 50 outliers final: 34 residues processed: 355 average time/residue: 0.1583 time to fit residues: 90.0529 Evaluate side-chains 347 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 307 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 16 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 272 optimal weight: 0.5980 chunk 280 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN B 652 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.160121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113824 restraints weight = 38525.649| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.42 r_work: 0.3227 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26178 Z= 0.135 Angle : 0.625 9.714 35754 Z= 0.296 Chirality : 0.045 0.205 4275 Planarity : 0.004 0.052 4368 Dihedral : 9.177 74.094 5620 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.99 % Allowed : 15.58 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 3042 helix: 1.63 (0.28), residues: 417 sheet: -0.67 (0.17), residues: 837 loop : -1.50 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 542 TYR 0.019 0.001 TYR C 173 PHE 0.023 0.001 PHE N 98 TRP 0.016 0.001 TRP P 35 HIS 0.005 0.001 HIS P 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (26022) covalent geometry : angle 0.57951 / 0.29 (35331) SS BOND : bond 0.00484 / 0.31 ( 45) SS BOND : angle 1.56744 / 0.95 ( 90) hydrogen bonds : bond 0.03635 / 2.44 ( 777) hydrogen bonds : angle 5.16914 / 3.53 ( 2259) link_ALPHA1-3 : bond 0.00842 / 0.44 ( 6) link_ALPHA1-3 : angle 2.97270 / 1.66 ( 18) link_ALPHA1-6 : bond 0.00512 / 0.35 ( 9) link_ALPHA1-6 : angle 2.10425 / 1.30 ( 27) link_BETA1-4 : bond 0.00682 / 0.52 ( 36) link_BETA1-4 : angle 2.31402 / 1.66 ( 108) link_NAG-ASN : bond 0.00400 / 0.25 ( 60) link_NAG-ASN : angle 2.36713 / 1.58 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 314 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 ASP cc_start: 0.8440 (t0) cc_final: 0.8178 (t0) REVERT: G 87 THR cc_start: 0.8752 (p) cc_final: 0.8543 (p) REVERT: H 77 GLN cc_start: 0.8026 (mt0) cc_final: 0.7769 (mp10) REVERT: L 27 THR cc_start: 0.4649 (m) cc_final: 0.4416 (t) REVERT: A 87 GLU cc_start: 0.7944 (mp0) cc_final: 0.7561 (mm-30) REVERT: A 129 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8470 (mt) REVERT: A 192 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8339 (ptt-90) REVERT: A 368 ASP cc_start: 0.7112 (t0) cc_final: 0.6891 (t0) REVERT: J 43 LYS cc_start: 0.7150 (mtmt) cc_final: 0.6941 (mmmm) REVERT: J 72 ASP cc_start: 0.8524 (t0) cc_final: 0.8266 (t0) REVERT: J 108 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8512 (tt) REVERT: K 77 GLN cc_start: 0.8091 (mt0) cc_final: 0.7703 (mp10) REVERT: M 31 ASN cc_start: 0.8670 (p0) cc_final: 0.8421 (p0) REVERT: M 53 GLN cc_start: 0.8963 (mp10) cc_final: 0.8311 (mp10) REVERT: M 79 GLN cc_start: 0.8267 (mp10) cc_final: 0.7739 (mp10) REVERT: N 27 THR cc_start: 0.4550 (m) cc_final: 0.4297 (t) REVERT: N 89 GLN cc_start: 0.5478 (tp40) cc_final: 0.5241 (tp40) REVERT: N 97 PHE cc_start: 0.6113 (t80) cc_final: 0.5876 (t80) REVERT: C 87 GLU cc_start: 0.7865 (mp0) cc_final: 0.7445 (mm-30) REVERT: C 129 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8441 (mt) REVERT: D 624 ASP cc_start: 0.8893 (m-30) cc_final: 0.8673 (m-30) REVERT: O 6 GLU cc_start: 0.8594 (mp0) cc_final: 0.8299 (mp0) REVERT: O 72 ASP cc_start: 0.8593 (t0) cc_final: 0.8143 (t0) REVERT: O 100 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8765 (ttmm) REVERT: P 77 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.7027 (mp10) REVERT: Q 31 ASN cc_start: 0.8738 (p0) cc_final: 0.8517 (p0) REVERT: Q 79 GLN cc_start: 0.8398 (mp10) cc_final: 0.8039 (mp10) outliers start: 53 outliers final: 39 residues processed: 354 average time/residue: 0.1576 time to fit residues: 89.4104 Evaluate side-chains 352 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 308 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain F residue 599 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 24 optimal weight: 0.0980 chunk 100 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 187 optimal weight: 0.0870 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN J 3 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS M 69 ASN ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.158427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111100 restraints weight = 38531.543| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.38 r_work: 0.3216 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 26178 Z= 0.206 Angle : 0.661 9.887 35754 Z= 0.314 Chirality : 0.046 0.222 4275 Planarity : 0.004 0.056 4368 Dihedral : 9.030 73.958 5618 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.10 % Allowed : 15.84 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 3042 helix: 1.47 (0.27), residues: 417 sheet: -0.73 (0.17), residues: 849 loop : -1.55 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 542 TYR 0.021 0.001 TYR C 173 PHE 0.022 0.002 PHE N 98 TRP 0.017 0.001 TRP P 35 HIS 0.006 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (26022) covalent geometry : angle 0.61422 / 0.30 (35331) SS BOND : bond 0.00498 / 0.32 ( 45) SS BOND : angle 1.64959 / 1.01 ( 90) hydrogen bonds : bond 0.03960 / 2.67 ( 777) hydrogen bonds : angle 5.23264 / 3.57 ( 2259) link_ALPHA1-3 : bond 0.00776 / 0.41 ( 6) link_ALPHA1-3 : angle 3.12430 / 1.74 ( 18) link_ALPHA1-6 : bond 0.00517 / 0.35 ( 9) link_ALPHA1-6 : angle 2.00875 / 1.23 ( 27) link_BETA1-4 : bond 0.00673 / 0.52 ( 36) link_BETA1-4 : angle 2.37187 / 1.69 ( 108) link_NAG-ASN : bond 0.00472 / 0.30 ( 60) link_NAG-ASN : angle 2.54412 / 1.70 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 307 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 ASP cc_start: 0.8456 (t0) cc_final: 0.8214 (t0) REVERT: H 77 GLN cc_start: 0.8026 (mt0) cc_final: 0.7760 (mp10) REVERT: I 79 GLN cc_start: 0.8285 (mp10) cc_final: 0.8045 (mp10) REVERT: L 27 THR cc_start: 0.4671 (m) cc_final: 0.4440 (t) REVERT: A 87 GLU cc_start: 0.7949 (mp0) cc_final: 0.7562 (mm-30) REVERT: A 129 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8494 (mt) REVERT: A 166 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8269 (ttp80) REVERT: A 192 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8343 (ptt-90) REVERT: J 72 ASP cc_start: 0.8554 (t0) cc_final: 0.8346 (t0) REVERT: J 108 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8494 (tt) REVERT: K 77 GLN cc_start: 0.8078 (mt0) cc_final: 0.7686 (mp10) REVERT: M 31 ASN cc_start: 0.8674 (p0) cc_final: 0.8384 (p0) REVERT: M 53 GLN cc_start: 0.9023 (mp10) cc_final: 0.8592 (mp10) REVERT: M 79 GLN cc_start: 0.8216 (mp10) cc_final: 0.7780 (mp10) REVERT: N 27 THR cc_start: 0.4708 (m) cc_final: 0.4435 (t) REVERT: N 89 GLN cc_start: 0.5531 (tp40) cc_final: 0.5275 (tp40) REVERT: N 97 PHE cc_start: 0.6127 (t80) cc_final: 0.5888 (t80) REVERT: C 129 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8372 (mt) REVERT: D 598 CYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8555 (m) REVERT: D 624 ASP cc_start: 0.8830 (m-30) cc_final: 0.8609 (m-30) REVERT: O 6 GLU cc_start: 0.8700 (mp0) cc_final: 0.8401 (mp0) REVERT: O 72 ASP cc_start: 0.8617 (t0) cc_final: 0.8232 (t0) REVERT: P 77 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7007 (mp10) REVERT: Q 31 ASN cc_start: 0.8747 (p0) cc_final: 0.8514 (p0) REVERT: Q 79 GLN cc_start: 0.8354 (mp10) cc_final: 0.7941 (mp10) outliers start: 56 outliers final: 44 residues processed: 346 average time/residue: 0.1724 time to fit residues: 95.3301 Evaluate side-chains 354 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 303 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain F residue 599 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 272 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 297 optimal weight: 0.9980 chunk 165 optimal weight: 0.0770 chunk 110 optimal weight: 0.0370 chunk 48 optimal weight: 0.0970 chunk 235 optimal weight: 0.4980 chunk 291 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 33 HIS B 652 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.161567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115616 restraints weight = 38404.995| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.49 r_work: 0.3265 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26178 Z= 0.108 Angle : 0.605 9.020 35754 Z= 0.290 Chirality : 0.044 0.199 4275 Planarity : 0.004 0.061 4368 Dihedral : 8.529 72.980 5618 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.73 % Allowed : 16.40 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 3042 helix: 1.86 (0.28), residues: 417 sheet: -0.50 (0.17), residues: 855 loop : -1.45 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG K 32 TYR 0.020 0.001 TYR C 173 PHE 0.023 0.001 PHE N 98 TRP 0.020 0.001 TRP P 35 HIS 0.004 0.001 HIS L 95B Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (26022) covalent geometry : angle 0.56522 / 0.28 (35331) SS BOND : bond 0.00385 / 0.25 ( 45) SS BOND : angle 1.38779 / 0.84 ( 90) hydrogen bonds : bond 0.03395 / 2.27 ( 777) hydrogen bonds : angle 5.03591 / 3.43 ( 2259) link_ALPHA1-3 : bond 0.00865 / 0.45 ( 6) link_ALPHA1-3 : angle 2.82680 / 1.58 ( 18) link_ALPHA1-6 : bond 0.00494 / 0.34 ( 9) link_ALPHA1-6 : angle 2.02056 / 1.23 ( 27) link_BETA1-4 : bond 0.00725 / 0.55 ( 36) link_BETA1-4 : angle 2.24389 / 1.63 ( 108) link_NAG-ASN : bond 0.00368 / 0.23 ( 60) link_NAG-ASN : angle 2.16896 / 1.44 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 322 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 ASP cc_start: 0.8382 (t0) cc_final: 0.8131 (t0) REVERT: H 77 GLN cc_start: 0.8046 (mt0) cc_final: 0.7807 (mp10) REVERT: L 27 THR cc_start: 0.4653 (m) cc_final: 0.4432 (t) REVERT: A 87 GLU cc_start: 0.7885 (mp0) cc_final: 0.7517 (mm-30) REVERT: A 129 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8431 (mt) REVERT: A 192 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8301 (ptt-90) REVERT: A 368 ASP cc_start: 0.7106 (t0) cc_final: 0.6891 (t0) REVERT: J 43 LYS cc_start: 0.7699 (mptt) cc_final: 0.7420 (pttm) REVERT: J 72 ASP cc_start: 0.8458 (t0) cc_final: 0.8221 (t0) REVERT: K 77 GLN cc_start: 0.8103 (mt0) cc_final: 0.7710 (mp10) REVERT: M 31 ASN cc_start: 0.8634 (p0) cc_final: 0.8421 (p0) REVERT: M 53 GLN cc_start: 0.8974 (mp10) cc_final: 0.8366 (mp10) REVERT: M 79 GLN cc_start: 0.8256 (mp10) cc_final: 0.7682 (mp-120) REVERT: N 27 THR cc_start: 0.4606 (m) cc_final: 0.4336 (t) REVERT: N 89 GLN cc_start: 0.5463 (tp40) cc_final: 0.5117 (tp40) REVERT: C 87 GLU cc_start: 0.7789 (mp0) cc_final: 0.7402 (mm-30) REVERT: C 95 MET cc_start: 0.8920 (ptm) cc_final: 0.8537 (ptt) REVERT: C 129 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8462 (mt) REVERT: D 624 ASP cc_start: 0.8892 (m-30) cc_final: 0.8673 (m-30) REVERT: O 6 GLU cc_start: 0.8502 (mp0) cc_final: 0.8254 (mt-10) REVERT: O 72 ASP cc_start: 0.8525 (t0) cc_final: 0.8099 (t0) REVERT: P 77 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6862 (mp10) REVERT: Q 31 ASN cc_start: 0.8690 (p0) cc_final: 0.8486 (p0) REVERT: Q 79 GLN cc_start: 0.8307 (mp10) cc_final: 0.7976 (mp10) REVERT: E 87 GLU cc_start: 0.7655 (mp0) cc_final: 0.7285 (mm-30) outliers start: 46 outliers final: 32 residues processed: 358 average time/residue: 0.1723 time to fit residues: 98.5538 Evaluate side-chains 345 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 309 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 33 HIS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 320 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 68 optimal weight: 0.9990 chunk 253 optimal weight: 8.9990 chunk 201 optimal weight: 0.0000 chunk 223 optimal weight: 9.9990 chunk 175 optimal weight: 8.9990 chunk 234 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 270 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 33 HIS B 543 ASN J 3 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 33 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.160814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114638 restraints weight = 38406.317| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.42 r_work: 0.3251 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26178 Z= 0.132 Angle : 0.611 9.177 35754 Z= 0.292 Chirality : 0.044 0.207 4275 Planarity : 0.004 0.054 4368 Dihedral : 8.295 72.566 5618 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.80 % Allowed : 16.40 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 3042 helix: 1.89 (0.28), residues: 417 sheet: -0.46 (0.17), residues: 819 loop : -1.44 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 542 TYR 0.019 0.001 TYR C 173 PHE 0.039 0.002 PHE N 97 TRP 0.019 0.001 TRP P 35 HIS 0.010 0.001 HIS H 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (26022) covalent geometry : angle 0.56890 / 0.28 (35331) SS BOND : bond 0.00409 / 0.26 ( 45) SS BOND : angle 1.51537 / 0.91 ( 90) hydrogen bonds : bond 0.03480 / 2.33 ( 777) hydrogen bonds : angle 5.00117 / 3.41 ( 2259) link_ALPHA1-3 : bond 0.00816 / 0.43 ( 6) link_ALPHA1-3 : angle 2.90062 / 1.62 ( 18) link_ALPHA1-6 : bond 0.00513 / 0.36 ( 9) link_ALPHA1-6 : angle 1.96190 / 1.21 ( 27) link_BETA1-4 : bond 0.00701 / 0.53 ( 36) link_BETA1-4 : angle 2.25267 / 1.63 ( 108) link_NAG-ASN : bond 0.00369 / 0.23 ( 60) link_NAG-ASN : angle 2.22252 / 1.48 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7911.49 seconds wall clock time: 136 minutes 0.70 seconds (8160.70 seconds total)